Variant Support View

The Variant Support View lists the SNPs and small InDels that were detected during SNP analysis. The bottom panel summarizes all the reads that span the selected variant location. Reads with identical sequences in the neighborhood of the selected SNP are clustered into a single row with the cluster size shown to the right. The cells can be colored by either base qualities or mapping qualities.

The image below shows the 10 bp neighborhood of a predicted C/T heterozygous SNP on chromosome 1. The SNP location is spanned by 191 reads. However, the bottom panel shows that all these reads can be grouped into just 11 distinct clusters based on their sequence in this 21 bp window. The small number of clusters in the window is an indirect indication that the error rate is fairly low.

The view with its sortable columns and cluster sizes is especially helpful in verifying heterozygous SNPs and SNPs that fall in high coverage regions. Large clusters with multiple variant positions can be used to detect haplotype blocks.